[PDF] Top 20 Estimation of alternative splicing isoform frequencies from RNA-Seq data
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Estimation of alternative splicing isoform frequencies from RNA-Seq data
... Early RNA-Seq studies have recognized that limited read lengths result in a significant percentage of so called multireads, ...estimated from unique reads and used to fractionally allocate ... See full document
13
Moderated estimation of fold change and dispersion for RNA seq data with DESeq2
... nate from each ...transcript isoform lengths change, and even in a wrong sign of LFCs in extreme cases ...to isoform- specific analysis, either through generalized linear mod- eling at the exon level ... See full document
21
Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data
... the frequencies, or expression levels, of different components do not interfere with each other, thus they can be analyzed ...same isoform and their weights are ... See full document
63
Innovative Algorithms and Evaluation Methods for Biological Motif Finding
... for isoform fre- quency estimation from any mixture of single and paired RNA-Seq ...current RNA-Seq ...derived from paired read data, but only for filtering ... See full document
105
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA seq data
... transcript isoform that generate just one transcript spe- cies are least accurately quantified by most methods ex- cept Scripture ...of isoform abundance estimation: maximum differences in accuracy ... See full document
26
The contribution of Alu exons to the human proteome
... and RNA-seq data of HeLa cells ...and RNA-seq reads to the up- stream, downstream, and exon-skipping splice junctions of Alu exons, and computed each Alu exon’s transcript inclusion ... See full document
14
The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence
... the Alternative Splicing Mutation Database (ASMD) – a collection of human exon sequences with short (1–6 nucleotides) internal mutations that change the balance of alternatively spliced mRNA isoforms or ... See full document
7
Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes
... extensive alternative splicing yielding nonsense mRNAs of clock genes is demonstrated beyond ...of alternative splicing in clock genes to the overall background in Arabidopsis? Is it the case ... See full document
15
Methods For Robust Quantification Of Rna Alternative Splicing In Heterogeneous Rna-Seq Datasets
... including RNA-seq, is not without its ...molecules from the original extract may not appear in the sequencer ...cDNA from both ends (paired-end sequencing) improves map- ping accuracy, but the ... See full document
98
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
... novel splicing events that it discovers in the mapped sequencing ...detected splicing differences such as which exon/junctions are involved, alternative splice type (skipped exon, mutually exclusive ... See full document
6
Profiling tissue-resident T cell repertoires by RNA sequencing
... information from RNA-seq datasets, and used it to characterize tumor-associated T cell ...mining RNA-seq datasets of varying read lengths, and provided a range of parameters for varying ... See full document
8
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer
... resulting from filtering are represented in yellow and final datasets in ...variants from this data against GRCh37 release of the reference human ... See full document
25
The Nonstructural NS1 Protein of Influenza Viruses Modulates TP53 Splicing through Host Factor CPSF4
... double-stranded RNA (15, 16), p85  for activation of phosphatidylinositol 3-kinase (PI3K) signaling (17), RIG-I, which inhibits the induction of the type I IFN response (IFN-I) (18–20), and cleavage and ... See full document
19
SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... Single-cell RNA sequencing (scRNA-seq) has revolution- ized cell biology, enabling studies of heterogeneity and transcriptome dynamics of complex tissues at single-cell ...scRNA-seq data is ... See full document
12
Genome-wide profiling of RNA editing sites in sheep
... detect RNA editing in sheep by comparing RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen ...sequence data filters, a total of 607 and ... See full document
9
Finding differential splice junctions in RNA-Seq data as transcriptional biomarkers for prostate cancer
... becoming RNA, and RNA becoming ...which from a helix-shaped double-stranded DNA sequence, a single stranded complementary RNA sequence is ...resulting RNA can be coding RNA or ... See full document
114
The U2AF1S34F mutation induces lineage specific splicing alterations in myelodysplastic syndromes
... Flow cytometry. To evaluate erythroid differentiation, cells were incubated for 30 minutes on ice with anti-CD36-PE (clone 5-271; BioLegend), anti-CD71-FITC (clone OKT9; eBioscience), and anti– CD235a-APC (clone HIR2; ... See full document
17
De novo assembly of bacterial transcriptomes from RNA seq data
... reflects the amount of RAM consumed during an assem- bly. A comparison of memory usage by SOAPdenovo2 and Trinity has been performed by others [27] and we did not repeat the analysis here. With default parameters, ... See full document
10
Next-generation profiling to identify the molecular etiology of Parkinson dementia
... support from NIH/National Institute of Neurological Disorders and ...honoraria from the Movement Disorder Society; has received publishing royalties from Humana Press; has been a consultant for ... See full document
10
A Short Isoform of Human Cytomegalovirus US3 Functions as a Dominant Negative Inhibitor of the Full-Length Form
... The individual products from alternatively spliced US3 transcripts do not affect the expression of MHC class I mol- ecules on the cell surface. The full-length US3 protein binds and retains MHC class I ... See full document
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